Wednesday, April 28, 2010

At least they weren't the only ones. The Toronto Star is a perfectly respectable newspaper. It's not one of those tabloids that publish anything in order to pander to the lowest common denominator.

But even a "respectable" newspaper can get taken in when it comes to religion. For some reason, the editors of this newspaper thought it was legitimate to publish a story on the latest announcement about the discovery of Noah's Ark [Noah’s Ark found, researchers claim]. They picked up on a story in a Chinese newspaper.

Anyone with an IQ over 100 knows there was no such thing as a world-wide deluge in 2800 BCE and there's no such thing as a giant ark built by some shepherd in Israel.

Science disproved that particular Biblical myth a long time ago. Whenever you see a story like this there are only two possibilities; either the "researchers" are making it up, or they were the victims of a hoax (or a bit of both). In this case, it seems to be mostly a hoax perpetrated on a gullible group who were only too willing to fall for it.

What about when a presumably respectable newspaper publishes something silly that flies in the face of everything we know about science and history? There's no excuse for that. Shame on The Toronto Star. Maybe they should hire a science journalist to save them from future embarrassment?

Sometimes you discover that you're related to people you'd rather not be related to. Here's a valid relationship between me and Richard Nixon.

Deborah Lockwood and her husband William Ward are my great9 grandparents. Deborah was born in Watertown Massachusetts in 1636 [see The Hanging of Goodwife Knapp in 1653]. William Ward was born in Fairfield Connecticut in 1631. Deborah's mother was Susanna Norman. There must be a million descendants of the Norman, Ward and Lockwood families. They're all related to Richard Nixon so I'm in good company.

Friday, April 23, 2010

I've been under the impression that the distinction between the fact of evolution and evolutionary theory is not controversial—at least among evolutionary biologists. Ever since Gould, the point has been that the facts of evolution include things like common descent and the history of life on Earth. Evolutionary theory attempts to provide a mechanism that accounts for those fact and observations.

Richard Dawkins makes this clear in his book The Greatest Show on Earth (p. 17).

Biologists often make a distinction between the fact of evolution (all living things are cousins) and the theory of what drives it (they usually mean natural selection, and they may contrast it with rival theories such as Lamarck's theory of 'use and disuse' and 'the inheritance of acquired characteristics'). ... Nowadays it is no longer possible to dispute the fact of evolution itself—it has graduated to become a theorum or obviously supported fact—but it could still bedoubted (just) that natural selection is its major driving force.

The distinction is important. Things like common descent and the history of life are the facts that demonstrate evolution. Evolutionary theory offers a solid, widely-accepted, explanation of how evolution happens.

Douglas Futuyma has written one of the most respected textbooks on evolution. He agrees with this distinction—as do all other textbook authors that I know of. Here's what Futuyma says in Evolution 2nd ed. p. 4.

The explanation of how modification occurs and how ancestors gave rise to diverse descendants constitutes the theory of evolution. We now know that Darwin's hypothesis of natural selection on hereditary variation was correct, but we also know that there are more causes of evolution than Darwin realized, and that natural selection and hereditary variation themselves are more complex than he imagined. A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitute our current theory of evolution or "evolutionary theory." Like all theories in science, it is a work in progress, for we do not yet know the causes of all of evolution, or all the biological phenomena that evolutionary biology will have to explain. Indeed, some details may turn out to be wrong. But the main tenets of the theory, as far as it goes, are so well supported that most biologists confidently accept evolutionary theory as the foundation of the science of life.

No doubt you're puzzled about the purpose of this posting. You are probably saying to yourself. "So what? We all know that, already."

Apparently, not all of us agree. In an otherwise excellent review of Richard Dawkin's book, Jerry Coyne says the following [see: The Improbability Pump].

Demonstrating the truth of natural selection is just one of Dawkins's aims, for the theory of evolution is composed of several more or less independent parts, which I like to describe in one longish sentence: "Life on earth evolved gradually, beginning with one primitive species; it then branched out over time, throwing off many new and diverse species--and the process producing the illusion of design in organisms is natural selection." This sentence constitutes a scientific theory, which is not just a guess but an informed statement about the general principles that explain many observations about nature.

I think that's very wrong. First, it's wrong because it states that the history of life is a theory. Second, it's wrong because it states that the "illusion of design" is part of modern evolutionary theory (it isn't). Third, it's wrong because it only mentions natural selection and modern evolutionary theory is much more than that.

I hope this was just an attempt to (over-)simplify evolution for the readers of The Nation. In that case it might be (just) excusable. But I can't wait until the creationists get a hold of this review. They'll be delighted to learn that, according to Jerry Coyne, the gradual descent and diversification of life is only a theory.

They'll also be happy to learn from a prominent evolutionary biologist that design is part of modern evolutionary theory.

Wednesday, April 21, 2010

Many of us struggle with the controversy between science and religion. As one who argues that science and religion are not compatible (with minor exceptions), I try hard to understand the views of my opponents. One of the greatest challenges is to understand why Francis Collins sees his position as an argument in favor of compatibility.

Here's a video of a talk he gave last October at The Veritas Forum in California. All of it is really interesting but the punchline comes at 50 minutes when he gives a short summary of his beliefs.

[First Slide] Almighty God, who is not limited in space and time, created a universe 13.7 billion years ago with its parameters precisely tuned to allow the development of complexity over long periods of time.

[Second Slide] God's plan included the mechanism of evolution to create the marvelous diversity of living things on our planet. Most especially, that plan included human beings.

[Third Slide] After evolution, in the fullness of time, had prepared a sufficiently advanced neurological "house" (the brain), God gifted humanity with free will and with a soul. Thus humans received a special status, "made in God's image."

[Fourth Slide] We humans used our free will to disobey God, leading to our realization of being in violation of the Moral Law. Thus we were estranged from God. For Christians, Jesus is the solution to that estrangement.

That's it. A very simple but, I think, entirely compatible view that does no violence either to faith or to science. And puts them in a harmonious position ...

Collins goes on to describe this view as "Theistic Evolution." It could also be called the "New Creationism."

I can think of six, perfectly scientific, questions that could be asked.

Is there any evidence of purposeful "fine tuning"?

Is there any evidence that humans were inevitable?

Is there any evidence of a Moral Law?

Is there any evidence of a soul?

Is there any evidence that humans have something called "free will" that other species lack?

Is there any evidence that such a personal God exists?

I think the answer to all six question is "no," therefore, believing those things conflicts with science. They are supposed to part of the natural, observable, universe and they should all be detectable, if they exist.

One of the distinguishing features of a true scientific controversy is that there are good arguments on both sides. In my class on controversies and misconceptions, I teach my students that they have to recognize a real scientific controversy and, when they do, they should be prepared to argue both sides. That's the only way to demonstrate that they understand the issues.

Unfortunately, this simple concept is not widely practiced—even among scientists. Quite often we see a case being made for one side without even acknowledging that there's plenty of evidence for the opposing view. I'm giving a talk on Monday about "Junk DNA" and that's one of the main points. The current literature is full of claims about the demise of junk DNA. The claim is based on some recent findings but nobody ever mentions the older evidence that has to be refuted. When you're advocating a new model you have to do two things: (1) present evidence in favor of our model, and (2) demonstrate that evidence against your model should be rejected.

You can't do one without the other.

This rule only applies to controversies within science. In many cases, the trick is to recognize a "real" scientific controversy from one that only appears to be a scientific controversy. Take Intelligent Design Creationism for example ....

I was thrilled to see a posting by Granville Sewell on one of the IDiot blogs. The title suggested that he was finally recognizing that science had some valid points in this non-scientific controversy [Acknowledging our opponents’ strong points]. My "thrill" rapidly turned to disgust when I read the posting ....

In any debate, it is always good strategy to acknowledge your opponent’s strongest points, thereby taking them off the table. In the debate over ID, our opponents have two very strong points:

1. We have discovered scientific explanations for so many other previously mysterious phenomena, why not evolution as well? The laws God made are very clever and fine-tuned, and probably are sufficient to explain everything in astronomy, geology, chemistry and atmospheric science, for example, so it is hardly surprising that many would insist that they must be able to explain all of biology as well.

2. There are a lot of things about the development of life that give the appearance of natural causes. “This just doesn’t look like the way God would create things,” is an argument frequently used by Darwin, and by modern day evolutionists. There are also things that don’t suggest natural causes–such as the sudden appearance of nearly all the animal phyla at the beginning of the Cambrian era–but much of the history of life admittedly does leave us with a strong impression of natural causes.

All of the “evidence” for evolution falls into one of these two categories, there is no evidence to support the idea that natural selection of random mutations or any other unintelligent process can explain the major steps of evolution. Once you have acknowledged these two strong points, our opponents have nothing.

Tuesday, April 20, 2010

I belong to the Committee for the Advancement of Scientific Skepticism (CASS) at the Centre for Inquiry—Canada. Members of that group have published an article about homeopathy on the National Post website: A vestige of the 18th century.

Congratulations to Mitchell Gerskup, Ryan Gray, Michael Kruse, Iain Martel and Justin Trottier for a great contribution to homeopathy awareness. And congratulations to the National Post for publishing it.

Monday, April 19, 2010

Charles Darwin died at Down house during the afternoon of April 19, 1882. Janet Brown describes the moment in her biography (Charles Darwin: The Power of Place p. 495).

He died on the afternoon of 19, April 1882, after sinking very low for two or three days beforehand and suffering what Emma called "fatal attack" at midnight on the 18th. There was no deathbed conversion, no famous last words. "I am not the least afraid to die," he apparently murmured to Emma. "Remember what a good wife you have been." Allfrey signed the death certificate giving "Angina Pectoris Syncope" as the cause of death, the gradual ceasing of the heart. He was seventy-three.

The subtitle of Janet Browne's book (The power of Place) alludes to the remarkable status that Darwin achieved following publication of On the Origin of Species. Darwin was buried in Westminster Abbey at a huge funeral held on Wednesday, April 26, 1882. He was buried next to Sir John Herschel near the tomb of Sir Isaac Newton, "... an honorable place but not as close to [Charles] Lyell as Emma had hoped" (Browne, p. 497).

George Campbell - The 9th Duke of ArgyllWilliam Cavendish - The 7th Duke of DevonshireEdward Henry Stanley - The 15th Earl of DerbyJames Russell Lowell - The American Ambassador to BritainWilliam Spottiswoode - Mathematician, physicist, the Queen's Printer, and friend of DarwinJoseph Dalton Hooker - Darwin's close friend and champion of his Theory of EvolutionThomas Henry Huxley - Darwin's close friend and champion of his Theory of EvolutionAlfred Russel Wallace - Darwin's friend and the co-founder of Natural SelectionSir John Lubbock - The 1st Baron of Avebury, Darwin's next door neighbor and close friend

Here's the report of the funeral published in The Times on Thursday, April 27, 1882 [Wikisource].

The Funeral of Mr. Darwin

The mortal remains of Charles Robert Darwin were interred in the Abbey at Westminster yesterday with marks of respect due to one whose name has been for many years familiar as a household word to his countrymen, and whose works have shed so much distinction upon English science. The coffin containing the body was brought to the Abbey late on the previous evening and borne through the cloisters, Mr. Darwin's five sons following, into the Chapel of St. Faith. This is a portion of the Abbey little known to casual visitors. It is a long narrow apartment, with a groined and vaulted roof, situate between the end of the south transept and the vestibule of the Chapter House, and was until a few years ago used as a store room, and for some time was mistakenly called the Chapel of St. Blaize. Sir Gilbert Scott, however, discovered at the east end, where traces of an alter are found, a mural painting of a female figure, evidently a saint, holding in her hands a book and an iron rod — the emblems of St. Faith. The western portion of the room formed of old a revestry. Into this bare chapel, which, to the eyes of of the greatest architect seemed "a picturesque and beautiful room," the coffin was carried on Tuesday night, and, seen by the dim light from two old-fashioned lanterns, the place seemed gloomy and tomb-like in contrast with the lofty, nobly proportioned interior of the Abbey which could be seen through the glass door opening into the south transept. The presence of death was more painfully forced on the mind even than during the solemn ceremonial of yesterday, when the great building was again peopled with the living. Soon after 11 in the morning those who were to follow the body as mourners began to assemble in the Chapter House. The Embassies of France, Germany, Italy, and Spain were represented, and among those invited through Messrs. T, and W. Banting to be present or to send representatives nearly all those who received invitations were present, were:—

At about 20 minutes to 12 the body was brought out of the Chapel of St. Faith, through the Chapter-house vestibule, into the west cloister, and the procession was formed. The coffin was covered with a black velvet pall edged with white silk, On it were laid many wreaths of beautiful white flowers, one of the wreaths having been sent by members of scientific societies in Liverpool, represented by Mr. Isaac C. Thompson, F.R.M.S., honorary secretary of the Microscopical Society of Liverpool. The pall-bearers were the Duke of Devonshire, the Duke of Argyll, the Earl of Derby, Mr. J. Russell Lowell, the American Minister; Mr. W. Spottiswoode, LL.D., President of the Royal Society; Sir Joseph Hooker, Mr. A. R. Wallace, Professor Huxley, Sir John Lubbock, and the Rev. Canon Farrar. Proceeding slowly along the south cloister those heading the procession were met at the west entrance by members of the family and others, whose names follow:—

Within the Abbey a large congregation was assembled, filling the seats on the south side of the nave, the seats in the choir and such as were not reserved for the mourners in the transepts, while a large number admitted without tickets stood on the north side of the nave. Among those present were the Baroness Burdett-Boutts and Mr. Burdett-Coutts, the Lord Mayor, and Lady Mayoress and Miss Ellis, Mr. Sheriff Ogg, the Rev. R. C. Billing, Mr. Mark H. Judge, Mr. L. T. D'Eyncourt, and the Head Constable of Westminster. Masters and Queen's scholars of the Westminster School also attended. At the West Cloister door the mourners were met by the Rev. Canon Prothero, as senior canon in the absence of the Dean, who is abroad. Canon Prothero having read the opening sentence of the Service for the Burial of the Dead, the choir changed the other processional sentences to the music of Croft, as the procession moved down the south aisle to the west end of the church and then up the nave into the choir. Following the choristers came the Rev. J. H. Cheadle and the Rev. J. Troutbeck (minor canons of Westminster), Canon Rowsell, Canon Barry, Canon Duckworth, and the Rev. S. Flood Jones (precentor), and near the senior canon the Chapter Clerk, Mr. C. St. C. Bedford. The body was placed in front of the Communion rails during the first portion of the service. The Psalms were chanted to Purcell's music, and after the Lesson, which was read by Canon Duckworth, an anthem composed for the occasion by Mr. Bridge was sung to the words from the Book of Proverbs, "Happy is the man that findeth wisdom. and getteth understanding. She is more precious than rubies, and all the things thou canst desire are not to be compared unto her. Length of days is in her right hand, and in her left hand riches and honour. Her ways are ways of pleasantness, and all her paths are peace." The soft and subdued ending of the composition, which was sung with much feeling by the choir, prepared the mind for the last sad duty that remained to be performed. The body was not removed to the grave, which is at the north-east corner of the nave next to that of Sir John Herschell, Dr. Bridge playing first Beethoven's Funeral March and then a more plaintive march by Franz Schubert in B minor, while the mourners proceeded to the grave, and the rest of the service was impressively read by Canon Prothero, the choir singing their part to Croft and Purcell's music. Near the grave and just beneath the monument to Sir Isaac Newton stood a remarkable and representative crowd of distinguished men, such as only an occasion of deep and general would bring together. Leaders of men and leaders of thought; political opponents, scientific co-workers; eminent discoverers, and practitioners of the arts. To name only a few as representative, there were Lord Spencer, President of the Council, who represented Her Majesty's Ministers at the funeral; the Marquis of Salisbury, Viscount Sherbrooke, Sir William Jenner, Sir Stafford Northcote, Sir Charles Dilke, Mr. Moncure D. Conway, Dr. Siemens, Sir William Gull, Mr. Childers, Professor Marshall, Sir John Hawkshaw, Mr. Ernest Hart, Mr. W. H. Smith, Mr. Herbert Spencer, Dr. Farquharson, Professor Flower, Mr. Robert Winthrop, and Mr. Ellis. The anthem by Handel, "His body is buried in peace, but his name liveth evermore," was sung, and the senior Canon having pronounced the Benediction, the mourners left, and the public were then allowed to pass round the grave. The inscription on the plate of the white, unpolished oak coffin read, "Charles Robert Darwin. Born February 12, 1809. Died April 19th, 1882."

In an article in to-day's Nature on the late Mr,. Darwin, Professor Huxley writes as follows:— "Not only in these islands, where so many have felt the fascination of personal contact with an intellect which had no superior, and with a character which was even nobler than the intellect, but in all parts of the civilized world it would seem that those who business it is to feel the pulse of the nations and to know what interests the masses of mankind were well aware that thousands of their readers would thin the world poorer for Darwin's death, and would dwell with eager interest upon every incident of his history. In France, in Germany, in Austro-Hungary, in Italy, in the United States, writers of all shades of opinion, for once unanimous, have paid a willing tribute to the worth of our great countryman, ignored in life by the official representatives of the kingdom, but laid in death among his peers in Westminster Abbey by the will of the intelligence of the nation. One could not converse with Darwin without being reminded of Socrates. There was the same desire to find some one wiser than himself; the same belief in sovereignty of reason; the same ready humour; the same sympathetic interest in all the ways and works of men. But instead of turning away from the problems of nature as hopelessly insoluble, our modern philosopher devoted his whole life to attacking them in the spirit of Heraclitus and of Democritus, with results which are as the substance of which their speculations were anticipatory shadows. The due appreciation or even enumeration of these results is neither practicable nor desirable at this moment. There is a time for all things—a time for glorying in our ever extended conquests over the realm of nature, and a time mourning over the heroes who have led us to victory. None have fought better, and none have been more fortunate than Charles Darwin. He found a great truth, trodden under foot, reviled by bigots, and ridiculed by all the world; he lived long enough to see it chiefly by his own efforts, irrefragably established in science, inseparably incorporated with the common thoughts of men, and only hated and feared by those who would revile, but dare not. What shall a man desire more than this? Once more the image of Socrates rises unbidden, and the noble peroration of the 'Apology' rings in our ears as if it were Charles Darwin's farewell:—'The hour of departure has arrived, and we go our ways—I to die and you to live. Which is the better God only knows.'"

We are requested to state that the absence of the Vice-Chancellor and members of the Council of the Senate of the University of Cambridge from the funeral of the late Mr. Darwin was occasioned by the circumstance that it was impossible for them to attend in consequence of the approaching election to the Regius Professorship of Hebrew. By the statute regulating the election it is imperative on the Vice-Chancellor and the members of the Council, who are the electors, to be present during the whole time each of the candidates for the Professorship delivers his exposition on the portions of Hebrew books assigned to him. The times for the delivery of these dissertations had been fixed nearly a month ago, and it was impossible to postpone them and to defer the election. Consequently, much to the regret of the Vice-Chancellor and the members of the Council, none of them could attend as representing the University of Cambridge.

Sunday, April 18, 2010

I don't watch Bill O'Reilly's show very often so I missed this segment. I find it extremely interesting that a major television network could air such a discussion in the 21st century. To me, it says something about popular views in American culture. It doesn't say that a majority of Americans agree with these idiots but it does say that their point of view is an acceptable part of the cultural mix. That's shocking.

The priest's comments are interesting from the perspective of the accommodationist wars. He claims that Roman Catholicism conflicts with all kinds of things, including socialism. Who knew?

[I haven't been keeping up with financial news. Is it true that Europe is in much worse economic shape that the USA? I didn't notice that during recent visits to Europe and the USA.]

I’m coyneing the term “New Creationism” to describe the body of thought that accepts Darwinian evolution but with the additional caveats that 1) it was all started by God, 2) had God-worshipping humans as its goal, and 3) that the evidence for all this is that life is complex, humans evolved, and the the “fine tuning” of physical constants of the universe testify to the great improbability of our being here—ergo God. New Creationism differs from intelligent design because it rejects God’s constant intervention in the process of evolution in favor of a Big, One-Time Intervention, and because these ideas are espoused by real scientists like Kenneth Miller and Simon Conway Morris. (Note that Miller, though, has floated the possibility that God does sometimes intervene in the physical world by manipulating electrons.) New Creationism is bad because, while operating under the deep cover of real science, it tries to gain traction for dubious claims about the supernatural.

This is pretty good but let's not insist that New Creationists have to postulate humans as the only goal of evolution. Some of them do and some of them are content with any kind of sentient being. The common characteristic is that they envisage some kind of purpose to the way the universe has unfolded.

"New Creationism" is a much better term than "Theistic Evolution" and I think I'll use it from now on. It has the advantage of putting the emphasis on "creationism," where it belongs. (Note, this is small-"c" creationism.)

Friday, April 16, 2010

This is the third in a series of postings by guest blogger, Arlin Stoltzfus. You can read the introduction to the series at: Introduction to "The Curious Disconnect". The first part is at: The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion. Arlin is challenging the status quo in modern evolutionary theory. He's not alone in this challenge but it's important to distinguish between kooks who don't know what they're talking about and serious thinkers who have something to say. Arlin is going to explain to you why everything you thought you knew about mutationism is wrong. In this article we learn about theories.

Before continuing with part 2, I would like to take a detour. Issues surrounding "evolutionary theory", and evolutionary theories, are going to be coming up again and again. In fact, I can see these issues emerging already in The Mutationism Myth. So, before we get bogged down in confusion and disagreement, I would like to begin a discussion of "theory" and "theories". We'll return to the Mutationism Myth next time.

Theory1 vs theory2

What does it mean to invoke "evolutionary theory"? Is "neo-Darwinism" (or "Darwinism") a theory, a school of thought, or something else? What gives a theory structure and meaning (e.g., axioms, themes, formulae)? What is the relationship between mathematical formalisms and other statements of "theory" (e.g., what does it mean for a lecturer to show a key equation of quantitative evolutionary genetics and assert "this is neo-Darwinism")? Who decides how a theory is defined, or redefined (e.g., is Ohta's "nearly neutral" theory an alternative to, or a variant of, Kimura's Neutral Theory of Molecular Evolution)?

Confusion regarding "theory" and "theories" is going to be an ongoing topic of attention in The Curious Disconnect. As noted in the Introduction, we're in an enormous muddle. The way to get out of this muddle is to take some time to build common understanding, learn some useful terms, and establish ground rules.

In this post, we'll begin the process of developing a shared framework for productively discussing "theory" and "theories". We will begin by addressing an ambiguity in the use of the word "theory", partly because this particular ambiguity is important, and partly as an exercise in addressing semantics. 0

Definitions

Dictionaries provide definitions that can be helpful to clarify the meanings of words and the complications of their usage. Definitions can be descriptive, telling us how a word is used, or prescriptive, telling us how it ought to be used. But, as most of us don't like to be told what we ought to do, I suspect that you share my belief in studying how words are used, in order to determine their denotations (what the word says) and connotations (what the word hints or implies). The English dictionaries used in America typically agree: the definitions that they provide reflect patterns of common usage, not the decrees of authorities.

A difficulty with dictionaries arises given that, within an isolated community, e.g., a scientific discipline, words can take on special meanings. So, dictionaries can be helpful, with the proviso that we need to be sensitive to the special use of terms within a discipline.

The discipline-specific use of a term can be nailed down by looking at examples of usage. For evolutionary biology, the discipline-specific use of a term is to be found in the research literature, and also in the secondary literature of monographs, textbooks, and other disciplinary writings.

Two meanings of "theory"

A good dictionary will distinguish several different senses of the word "theory", including the following two that I believe are the most relevant for our discourse:

1) a major conjecture or systematic hypothesis to account for observed phenomena, as in "prion theory of disease" or "Lamarck's theory of evolution";

2) the body of abstract principles relevant to some discipline, methodology or problem area, as in "music theory" or "population genetics theory"

That is, a theory1 is a grand hypothesis, a conjecture about the actual world, while a theory2 is a collection of principles or models or other formalisms that might apply only in an imagined world. Fisher (1930) famously said that "No practical biologist interested in sexual reproduction would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should he do if he wishes to understand why the sexes are, in fact, always two?" Theoreticians aren't necessarily good with facts, so we'll ignore that the sexes (in the sense of mating types) are not, in fact, always two. Fisher clearly encourages us to work out formalisms for imagined or hypothetical cases. The collection of all these models or formalisms about sexes would constitute the theory2 of sexes. A theory1 of sexes might propose a causal explanation for the actual historic phenomenon of the origin and maintenance of sexual reproduction in animals, addressing such issues as the heterogametic basis of sex determination. 1

These two meanings are not just recognized in dictionaries, but are established in scientific usage. Gilbert's "Exon Theory of Genes" (Gilbert 1987) is the conjecture that genes evolved from exons (i.e., large protein-coding genes emerged by joining primordial exon-minigenes). The prion theory1 of disease clearly revolves around a conjecture that there are actual diseases caused by actual prions. By contrast, population genetics theory2 is not the conjecture that populations have genetics; likewise, the theory2 of stochastic processes is not a conjecture that stochastic processes occur, but consists of a body of abstract principles that might be applicable to such stochastic processes as might occur in some actual or imagined universe.

The use of the abstract noun, as in "let's talk about theory" as opposed to "let's talk about { a | the | this } theory", often signals the use of theory2. For instance, the title of a report by the National Academy of Sciences on "The Role of Theory in Advancing 21st Century Biology" signals a likely emphasis on theory2, and indeed, the report emphasizes the development of formalisms more than conjectures, and says that "a useful way to define theory in biology is as a collection of models", clearly a reference to theory2. The report also mixes in some references to theories1.

Obviously, there is a connection between scientific theories1 and scientific theory2. One way of thinking about the connection is that the abstract principles of theory2, when suitably limited by measurable or observable quantities from the actual world, can provide the basis of a theory1, and conversely, theories1 draw on theory2 for logical structure. Kimura's Neutral Theory (Kimura 1983) provides a clear example because the theory1 and theory2 were developed separately: Kimura combined pre-existing theory2 (of stochastic population genetics) with the concrete assertion that the values of certain quantities (relating to population sizes and mutant effects) were such that, for DNA and protein sequences, neutral evolution by mutation and random fixation would be far more common than anyone had imagined previously. The definition of effectively neutral alleles (perpetually misunderstood by critics) and the probability of fixation under pure drift were known to the canonical founders of population genetics ((Wright 1931); ch. IV of (Fisher 1930); appendix of (Haldane 1932)). Another indication of the distinctness of theory1 and theory2 is that opponents of the Neutral Theory1, who deny the truth of the theory1, are nonetheless quite happy to make use of its theoretical2 infrastructure (Kreitman 1996).

Development and application of theory1 and theory2

We treat the two kinds of "theory" differently, and rightly so.

A theory1 contains a major supposition or unproved conjecture about the world. Kimura's Neutral Theory is the conjecture that most changes at the "molecular level" represent the random fixation of effectively neutral alleles. Darwin proposed, but could not prove, that all large-scale evolutionary changes were built from infinitesimal increments of change that emerged by a process of hereditary "fluctuation". A theory1 takes risks: in Popperian terms, its subject to empirical refutation; in the words of Huxley, a beautiful theory1 can be "killed by an ugly fact."

The relevant standard of validity for theory2 is not verisimilitude (trueness to life), but consistency: the principles derived in the theory are consistent with its assumptions. Importantly, new principles added to a body of theory2 are consistent with previous principles, except in the sense that a body of theory2 may be subdivided into branches that cover non-overlapping universes. If they are not, a logical error has occurred.

While new theory2 is consistent with existing theory2, theories1 often stimulate interest precisely because they conflict with previous theories1. Of course theories1 strive to be internally consistent, but in biology at least, theories1 are not axiomatic, and often encompass ambiguities that make rigorous analysis difficult. A theory1 can be brought down by a contradiction that arises internally, e.g., one part can be found to contradict another part.

While a theory1 is about the actual world, and thus is judged by verisimilitude, principles of theory2 need not apply to the real world. Indeed, no amount of conflicting data will cause us to discard a principle of theory2 that is properly derived: a beautiful piece of theory2 cannot be killed by an ugly fact. Fisher's fundamental theorem either is logically valid or is not logically valid, independent of any facts.

Digressions

The distinction between theory1 and theory2 is hidden in the ambiguous word "theory", but I think it comes out more clearly in specific word-derivatives and grammatical usages that seem to favor one meaning more than the other. I mentioned above that the abstract noun typically signals theory2. I'm also convinced that when we refer to a "theoretician", we typically do not mean someone like Tom Cavalier-Smith whose scientific output consists of bold conjectures or systematic hypotheses (we might call such people "theorizers"), but instead someone like Joe Felsenstein whose work focuses on mathematical or algorithmic foundations, i.e., theory2. Its a rare scientist, it seems to me, who is productive both as a theoretician and as a theorizer (e.g., Kimura, Hamilton).

Neither meaning of theory would cause us to relinquish the label "theory" for a proposition that lacks verisimilitude. Clearly the propositions of theory2 do not have to apply to the real world. And a theory1 is a conjecture, not necessarily a true conjecture. Thus, even opponents of the Neutral Theory1, who believe that the theory does not fit the actual world, still refer to it as The Neutral Theory (Kreitman 1996).

I mention this because there is an absurd tendency in the literature of evolution advocacy, e.g., NCSE's screeds, to say that, because scientists reserve the word "theory" only for constructions that have been extensively verified and are accepted as true, the use of "theory of evolution" among scientists means that evolution is well supported.

This argument clearly is false, and the proof does not depend on the theory1 vs. theory2 distinction, but only on the fact that scientists habitually choose to refer to Kimura's theory or Lamarck's theory or Gilbert's theory as a "theory", even if its known to be wrong or is considered deeply suspect. This pattern holds, not just in biology, but in other disciplines. In astronomy, the geocentric theory remains a theory though it has been abandoned; in physics, the phlogiston theory, or the aether theory of light propagation (roughly, the theory that space must be substantive in order for waves to propagate in it) remain theories even though they were abandoned. So, write to the NCSE and tell them to stop using this lame argument. Really, we can do better than that.

The NCSE fallacy seems to arise from mixing together the proposed explanation of phenomena aspect of theory1 and the accepted as valid aspect of theory2. This is suggested from the way that NCSE's screed cites the NAS report on theory2 (the same one that I quoted above) as though it provided a definition of theory qua "well substantiated explanation", which definitely is not the same as "collection of models".

Lets try to sort this out in terms of the distinction between theory1 and theory2. Evolutionists have recourse to a body of theory2 (formalisms or models or principles), ranging from purely phenomenological models of branching and character-state change used in phylogenetics, to the breeder's equation used in quantitative genetics, to detailed formulas for population-genetics processes, and so on. We accept the validity of these abstractions in the theory2 sense of validity, i.e., we accept that they are derived without error, so as to be logically consistent with their assumptions. This body of abstractions, principles, or formalisms (in NAS parlance, this collection of models) is evolutionary theory2.

But saying that this theory2 is valid is not at all the same thing as claiming that its true in the sense of verisimilitude; and claiming that it has verisimilitude is not the same as saying that its complete, in the sense of sufficiently accounting for the phenomena of evolution. For instance, the theory2 of quantitative evolutionary genetics is based on the assumption of infinitesimal variation, but the theory2 itself does not claim that all traits, nor even any single trait, evolved in this manner-- that would be a theory1 issue. Kimura's diffusion equations are a part of population genetics theory2 that provides a way to work out the probability of fixation of alleles under ideal conditions, but it doesn't assert that the results are applicable to any particular case. Got it?

Homework

The wikipedia entry on theory (http://en.wikipedia.org/wiki/Theory) has a "List of Notable Theories" that clearly mixes up theories1 or grand conjectures (the cell theory, the phlogiston theory) with theories2 or bodies of abstract principles (music theory, extreme value theory). What are some other clear examples of theory1 and theory2 in this list? Which examples are difficult to classify (and what does one learn from those)?

Who, besides Kimura and Hamilton, was productive as both a theoretician and as a theorizer?

Think of a few theories in science, ideally in life sciences. I'm going to assert that they are not axiomatic, i.e., they are not completely encompassed by precisely stated propositions. Given this, how do we really know what defines the theory? If we know a theory from the verbal statements in a body of literature (i.e., "things people say"), what is the relationship of an individual expression (e.g., a paper, a monograph, a quotation) to the theory? Is it the instantiation of a platonic form or essence? How do we get to the essence? Is the distribution of expressions of a theory its "reaction norm", representing environmental noise in the expression of an underly structure (the theory's "genotype")?

The Modern Synthesis as theory1: into the memory hole

The folks at NCSE and wikipedia are not the only ones blurring the issues. The Modern Synthesis or modern neo-Darwinism 2 was put forth originally as a falsifiable theory1 of evolution, but evolutionists themselves don't treat it that way anymore. For instance, in Maynard Smith's defense of "neo-Darwinism" (Maynard Smith 1969), the only kinds of falsifying observations he can imagine are cases that seem to introduce supernatural forces, e.g., if the spots on a fish always appeared in prime numbers, he says this would contradict neo-Darwinism. He does not imagine variation-induced trends, discontinuous jumps based on individual mutations, or extensive neutral evolution as contradictions of "neo-Darwinism", though these ideas were rejected by the architects of modern neo-Darwinism. Maynard Smith makes the claim in regard to the Neutral Theory that "I have never seen any reason why, as a naive Darwinist, I should reject this theory" (Maynard Smith 1995). It seems that, for Maynard Smith, "neo-Darwinism" is not a theory1 at all, but merely indicates a commitment to scientific materialism, i.e., seeking natural causes through observation and experiment.

Other authoritative sources suggest that the Modern Synthesis is no longer viewed as a falsifiable conjecture. In Hull's Encyclopedia of Evolution article on the history of evolutionary thought (Hull 2002), the Modern Synthesis is presented as an open-ended "theory" that merely assumes the principle of selection and the rules of genetics, and which has swallowed up the neutral theory along with all other useful ideas:

"Any criticism of the synthetic theory that turned out to have some substance was subsumed in a modified version of this theory. Instead of being a weakness, this ability to change is one of the chief strengths of the synthetic theory of evolution. As in the case of species, scientific theories evolve" (p. E16)

Hull's conception of the Modern Synthesis sounds more like an extensible set of principles, theory2, than the theory1 of Mayr, Simpson, Ayala, etc (which is extensible in some ways but closed and falsifiable in others). I'm not necessarily going to say its wrong for scientists to decide that the Modern Synthesis is no longer a theory1, but can someone please tell me when, and on what basis, did we make this decision? Is there a citation for that? And who decided that we wouldn't tell Richard Dawkins, leaving the poor fellow stuck in a time warp defending the original Modern Synthesis? 3

But I'm getting ahead of myself. I started The Curious Disconnect with the The Mutationism Myth because 1) most evolutionists don't understand how the Modern Synthesis came into existence as a theory1 that entails risky conjectures, and 2) the mutationist challenge provides the definitive historical proof that the Modern Synthesis is a theory1 and not just a commitment to selection and the rules of genetics. The historical record will show clearly that the mutationists or "Mendelians" presented a workable synthesis of selection and the rules of genetics, and that their view was rejected by the architects of the Modern Synthesis. Once we find out why, we will understand what makes the Modern Synthesis a theory1.

Maynard Smith, J. 1995. Life at the Edge of Chaos? Pp. 28-30. New York Review of Books, New York.

Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97.

Notes

0I thank Dr. Mike Coulthart for originally drawing my attention to the importance of this distinction.

1If we were to propose just that the sexes are always 2 in number, simply because that is what we have seen in the past, I would call this an empirical generalization or "law". Sometimes "theory" is used for such a generalization, but that usage does not correspond to either meaning of "theory" addressed here.

2I'm using "modern neo-Darwinism" as a synonym for "Modern Synthesis". Neo-Darwinism (for our purposes, Darwinism 1.2) is the pre-Mendelian theory of Weissman and Wallace emphasizing the supreme power of selection and infinitesimal variation to build adaptation (and rejecting Darwin's reliance on Lamarckism). The Modern Synthesis (Darwinism 2.0) comes from this tradition and is often called "neo-Darwinism", though "modern neo-Darwinism" is clearer.

3Kidding aside, its quite useful to have a scholar still defending the actual Modern Synthesis. For instance, in his attempt to rebut Behe (Dawkins 2007), Dawkins claims that mathematical geneticists "have repeatedly shown that evolutionary rates are not limited by mutation" and that Behe's critique based on the idea that evolution depends on specific mutations would mean that "the entire corpus of mathematical genetics, from 1930 to today, is flat wrong". In making this claim, Dawkins is correctly representing the Modern Synthesis view that (due to the buffering effect of the "gene pool") evolution does not depend on the rate of new mutations, a principle that he believes to be an infallible theoretical result.

Wednesday, April 14, 2010

Elaine Howard Ecklund is a sociologist at Rice University; we cited her work on the topic of science and religion in Unscientific America. Now, she is out with a book that is going to seriously undercut some widespread assumptions out there concerning the science religion relationship.

Unfortunately, Chris doesn't present any data because he's not a scientist. Data really isn't his thing.

I don't have a copy of the book so I can't check it myself. Fortunately, Razib Khan, one of Chris Mooney's fellow bloggers on the Discover website, was able to find some of the data [Scientists as “spiritual atheists”].

Let's be clear about one thing. This is not a poll of scientists. It's a poll of American scientists. The title of Ecklund's book, Science vs Religion: What Scientists Really Think, is somewhat misleading.1 Here's two charts from the book.

Hmmm ... none of my assumptions have been undercut. How about yours?

I guess what Chris Mooney means is that some of his assumptions will have to be re-evaluated. It's about time.

1. Unless you're an American. Then you probably believe that all scientists live in the USA.

Michael Ruse has criticized Alvin Plantinga for being critical of evolution. Plantinga defends himself in a letter published in The Chronicle of Higher Eduaction: Evolution, Shibboleths, and Philosophers.

I want to address one particular point that Plantinga makes because it's relevant to the issues that come up in the accommodationist wars.

"Why," asks Ruse, "does Plantinga feel this way?" Because, he says, "In his view, Darwinism implies that there is and can be no direction in life's history." Still another missed distinction. As far as I can see, God certainly could have used Darwinian processes to create the living world and direct it as he wanted to go; hence evolution as such does not imply that there is no direction in the history of life. What does have that implication is not evolutionary theory itself, but unguided evolution, the idea that neither God nor any other person has taken a hand in guiding, directing or orchestrating the course of evolution. But the scientific theory of evolution, sensibly enough, says nothing one way or the other about divine guidance. It doesn't say that evolution is divinely guided; it also doesn't say that it isn't. Like almost any theist, I reject unguided evolution; but the contemporary scientific theory of evolution just as such—apart from philosophical or theological add-ons—doesn't say that evolution is unguided. Like science in general, it makes no pronouncements on the existence or activity of God.

Plantinga is allying himself with Eugenie Scott and other accommodationists who fiercely defend the idea that science can't address issues such as purpose. In fact, Genie fought hard to remove references to "unsupervised, impersonal, unpredictable and natural process" from a statement on evolution by the National Association of Biology Teachers back in 1995 [NCSE v National Association of Biology Teachers].

I disagree with Plantinga, and with the National Center for Science Education. The idea that evolution might be guided by God is a legitimate question for scientists to address. After all, if it's true then parts of evolutionary theory might have to be revised. I do not accept the claim that scientists must avoid this question because it comes from religion.

When you are thinking like a scientist there's only one possible conclusion. There is no scientific evidence to support the hypothesis that the history of life on Earth was guided by God. Everything we know about the history of life is consistent with an entirely natural process—one that's characterized by chance and contingency. It is perfectly reasonable as a scientist to state this position clearly. This is not stepping outside of the boundaries of science.

Let me explain my position by using an analogy. Imagine the claim that aliens visited the Earth 3.5 billion years ago and seeded our planet with cyanobacteria. After much investigation scientists find no support for such a claim. Is it legitimate for them to conclude that aliens are not responsible for life on Earth? Of course it is. All scientists know that you can't prove a negative but that doesn't mean you can't assign probabilities and behave accordingly.

Philosophers aren't likely to get upset if scientists make statements denying that aliens are responsible for life as we know it. That's because belief in alien visitors isn't one of those kooky ideas that demands special status. However, if scientists make the more general claim that life appears to have evolved by purely natural processes then this gets their dander up. All of a sudden science is threatening religion and this is not allowed. It's "philosophical naturalism" and not "methodological naturalism." It's not science according to Plantinga and many accommodationists, including Michael Ruse. Bollocks, I say.

Scientists call it as they see it. If that upsets the theists then they had better learn to deal with it instead of whining about the science being illegitimate.

Science says that evolution is not divinely guided, based on what we know today.

I've got a confession to make. I've been posting about homeopathy this week but everything I've said has been negative. You know there must be another side to this "controversy" so in the interest of fairness, here it is. These homeopaths are putting forward the best possible case for taking homeopathic "remedies."1

Tuesday, April 13, 2010

This gets better and better as the week goes on. PZ Myers has discovered a company that markets fragments of DNA to promote good health. You don't actually eat the DNA, instead you drink water that has been exposed to the DNA [More Magic Snake Oil].

The company is called Homeovitality® and one of their products is Super Memory/IQ. I'm showing a picture of the product taken from their website in order to prove to you that it actually exists. This is part of the discussion concerning its scientific/medical efficacy—an important part of science education and social responsibility.

How does it work? Before I explain it to you, you'd better be sitting down. Try and remain calm.

There are two genes in your genome called CRM2 and SNAP-25. CHRM2 encodes a muscarinic receptors and various alleles of this gene have been associated with alcohol dependence and drug dependance, according to the Online Mendelian Inheritance in Man (OMIM) database [CHOLINERGIC RECEPTOR, MUSCARINIC, 2; CHRM2]. SNAP-25 encodes a synaptosomal-associate protein of 25kDa molecular weight. There have been reports that alleles of SNAP-25 are associated with hyperactivity but a separate study did not confirm this association according to OMIN [SYNAPTOSOMAL-ASSOCIATED PROTEIN, 25-KD; SNAP25].

Homeovitality® had some DNA sequences made for each of these genes: a 164 bp fragment in the case of CRM2 and a 144 bp fragment in the case of SNAP-25 [What is Homeovitality®?]. They used these pieces of DNA to make the Super Memory/IQ product.

Homeovitality® products have also been succussed at each dilution stage so they will also help to promote desirable forms of hybrid vigour in a “like promotes like” mode of action involving some of the mechanisms (4) described by Dr. Kratz, (http://kulisz.com/how_does_homeopathy_work.htm).

Homeovitality® products are safe because firstly, they are used at similar dilutions to classical homeopathic disease remedies and secondly, hybrid vigour is a completely natural biological process that has been developed by nature over millions of years to enable all creatures to enjoy “super health” and disease resistance.

"Succussed refers to the practice of forcefully striking the various dilution solutions in order to help "potentize" the effect. "Hybrid vigor" refers to the belief that these DNA sequences—or, more appropriately, the memory of these sequences—will produce heterozygosity in patients and that's a good thing.

Monday, April 12, 2010

Robert Alexander Hood1 was born in 1895 in a small village north-west of Waterloo, Ontario, Canada. He went to France in 1916 when he was only 21 years old. Robert fought with the 73rd Battalion and he was killed in action at Vimy Ridge on this day, April 12, in 1917.

Canadians "celebrate" the battle of Vimy Ridge as a great Canadian victory. It was part of the larger Battle of Arras, which in turn was a diversionary attack in support of the larger Nivelle Offensive carried out by the French Army. About 3,600 young Canadian men were killed during the four day battle and 7,000 more were wounded. This is just a small fraction of the casualties on both sides during World War I.

We need to be very careful not to glorify war while remembering all those young mean and women who died in a war that never should have been fought. I will eventually go to Arras and visit the large memorial erected by the Canadian government (see below) but I will do it in order to reinforce my view that war is folly and the deaths of soldiers like Robert Alexander Hood should never have happened.

There is never any glory in war and it's nothing we should ever be proud of.

Are all homeopaths and their supporters complete idiots? Do they all think they're practicing some form of black magic? No, they usually don't think that at all. Many of them honestly believe that there's scientific evidence supporting homeopathy. They actually believe that water can retain some magical properties after it has been exposed to certain chemicals. How is this possible? It's because of "nanobubbles."

Here's John Benneth explaining the "science" behind homeopathy. This is woo of the highest order. Read Orac's take-down at Your Friday Dose of Woo: The physics of homeopathy and "nanocrystalloids". There are no reputable scientists who believe what John Benneth claims. If he's implying that there's scientific support for homeopathy, then what he's saying is not true.

Me and my Christian friends have a lot in common but I didn't realize how much until I found this site: Gods You Don't Believe In. It lists about 2,800 gods of various sorts. I don't believe in any of them and most Christians reject all but a handful1. That makes about 2,795 gods whose nonexistence we agree on.

1. I'm not sure how to count up the gods of Christianity. If you assume that the big guy, Jesus, and the ghost are all the same person then what about Satan and some of the senior angels like Gabriel and Michael? Do they count as gods? And what about the other gods mentioned in the ten commandments? The god of the Bible says not to worship them because he is jealous but he doesn't deny that they exist. Who are they?

Homeopathy awareness week is coming up and scientists from all around the world are gearing up to explain why homeopathy doesn't work—that's why it's called "alternative" medicine. It's a part of quack medicine that's not "real" medicine. Real medicine is based on scientific evidence.

Many people don't know what homeopathy is all about. They confuse homeopathy with a host of other forms of non evidence-based medicine like naturopathy and herbalism. That's a big mistake. Homeopathy is a form of treatment where you drink water that supposed to contain the magical imprint of some chemical. The chemical is often quite dangerous but, don't be worried, it's not really present in the treatment you pay for.

Homeopathy (also spelled homoeopathy or homœopathy) is a form of alternative medicine, first proposed by German physician Samuel Hahnemann in 1796, that attempts to treat patients with heavily diluted preparations. Based on an ipse dixit[1] axiom[2] formulated by Hahnemann which he called the "law of similars", preparations which cause certain symptoms in healthy individuals are given as the treatment for patients exhibiting similar symptoms. Homeopathic remedies are prepared by serial dilution with shaking by forceful striking, which homeopaths term "succussion," after each dilution under the assumption that this increases the effect of the treatment. Homeopaths call this process "potentization". Dilution often continues until none of the original substance remains.

Don't confuse it with anything else. There's absolutely no evidence that homeopathy works. The scientific data, taken as a whole, is conclusive. Be wary of those who believe in homeopathy because their advice on other forms of treatment may not be based on evidence either. Homeopathy is bad enough but it often keeps even worse company.

Wednesday, April 07, 2010

As most of you know, the citizens of the United Kingdom do not obsess over the separation of church and state and they do not use their constitution to keep creationism out of their schools. That's why the question posed by Michael Reiss in New Statesman is a valid one in that country, "Should creationism be taught in British classrooms?". The answer might surprise many people in other countries.

Why schools and universities should encourage debate on evolution -- and how this could benefit science.

.... When teaching evolution, there is much to be said for allowing students to raise any doubts they have in order to shape and provoke a genuine discussion. The word "genuine" doesn't mean that creationism and intelligent design deserve equal time with evolution. They don't. However, in certain classes, depending on the teacher's comfort with talking about such issues, his or her ability to deal with them, and the make-up of the student body, it can and should be appropriate to address them.

Having said that, I don't pretend to think that this kind of teaching is easy. Some students become very heated; others remain silent even if they disagree profoundly with what is said. But I believe in taking seriously the concerns of students who do not accept the theory of evolution while still introducing them to it. Although it is unlikely that this will help them resolve any conflict they experience between science and their beliefs, good teaching can help students to manage it - and to learn more science.

My hope is simply to enable students to understand the scientific perspective with respect to our origins, but not necessarily to accept it. We can help students to find their science lessons interesting and intellectually challenging without their being a threat. Effective teaching in this area can help students not only learn about the theory of evolution, but also better appreciate the way science is done, the procedures by which scientific knowledge accumulates, the limitations of science and the ways in which scientific knowledge differs from other forms of knowledge.

I agree with this point of view. I think the main arguments for creationism, and against evolution, should be discussed in science class. It's an excellent way of showing what real science is and how it should be practiced.

The problem with ignoring the main criticisms of evolution is that students are going to hear about them from other sources and they won't know what to think about those points of view unless we teach them how to reason. The goal of science education is to teach students how to think, not just fill them with facts. It's our responsibility as teachers to teach critical thinking. One of the best ways to do that is to give them some popular examples to discuss and debate.

Some bloggers are huge fans of genetic testing. They frequently post articles promoting one of the private companies that charge you for doing these tests. ScienceRoll recently posted this video of Anne Wojcicki making a pitch for her company. Wojcicki is one of the co-founders of 23andMe. It's interesting to see how she mixes various rationales for genetic testing with a pitch for 23andMe.

Imagine this was a talk by the CEO of a major pharmaceutical company about the importance of their drugs and why you should buy them. We would probably be more skeptical than we seem to be about Ann Wojcicki. Why is that?

Tuesday, April 06, 2010

World Homeopathy Awareness Week takes place next week (April 10-16). This is a week devoted to making people aware of homeopathy and our local Centre for Inquiry and the Committee for Advancement of Scientific Skepticism (CASS) is planning to take full advantage of the opportunity. We'd like everyone to know there's no scientific evidence that supports homeopathic "cures" and, furthermore, the fundamental principle behind homeopathy conflicts with everything we know about modern science.

I urge all bloggers to post something next week in order to let the public know about this scam.

The Canadian Society of Homeopaths also has a number of events planned but I don't think they're talking about the same kind of "awareness."

HOMEOPATHY AND MENTAL WELL-BEING: BODY AND MIND IN BALANCE

The theme of the 2010 Homeopathy Awareness Month is Homeopathy and Mental Well-being: Body and Mind in Balance. As in previous Awareness celebrations, Registered and Associate members of the Canadian Society of Homeopaths will sponsor events, displays, and special promotions in their communities across Canada.

Canadian troops and support personal have been in Afghanistan for the better part of ten years. The goal was to create a stable democratic state that could offer security to its citizens and promote the rights and values that we cherish in Western democracies.

We aren't any closer to achieving that goal than we were ten years ago. Should Canadian forces remain in Afghanistan after 2011?

There are two main options ....

1. cut and run (withdraw all military forces)2. soldier on, perhaps with no combat troops

I favor option #1. We've given it our best shot and it's time to admit defeat. Afghanistan is not going to become a respectable member of the world's democratic community.

America has spent more than $6 billion since 2002 in an effort to create an effective Afghan police force, buying weapons, building police academies, and hiring defense contractors to train the recruits—but the program has been a disaster. More than $322 million worth of invoices for police training were approved even though the funds were poorly accounted for, according to a government audit, and fewer than 12 percent of the country's police units are capable of operating on their own. Ambassador Richard Holbrooke, the State Department's top representative in the region, has publicly called the Afghan police "an inadequate organization, riddled with corruption." During the Obama administration's review of Afghanistan policy last year, "this issue received more attention than any other except for the question of U.S. troop levels," Holbrooke later told NEWSWEEK. "We drilled down deep into this."

The worst of it is that the police are central to Washington's plans for getting out of Afghanistan. The U.S.-backed government in Kabul will never have popular support if it can't keep people safe in their own homes and streets. Yet in a United Nations poll last fall, more than half the Afghan respondents said the police are corrupt. Police commanders have been implicated in drug trafficking, and when U.S. Marines moved into the town of Aynak last summer, villagers accused the local police force of extortion, assault, and rape.

It's time to leave—the sooner the better. The people of Afghanistan have to want change bad enough to fight for it and that's ain't happening.

Monday, April 05, 2010

You've been following the battles in the Accommodationist Wars for several years. If you've been paying attention you will by now have acquired a good understanding of the main arguments on both sides. You should be able to recognize which arguments are valid and which ones are false—in terms of their logic.

Now it's time for the test.

Read the following passage by Michael Zimmerman1 on The Huffington Post. He is defending the proposition that the evolution/creation controversy is not a conflict between science and religion [Redefining The Creation/Evolution Controversy]. Your task is to identify the logical flaw(s) in this argument. For the purposes of this test, we're not interested in who's right and who's wrong in the Accommodationist Wars. I'm just interested in knowing whether you can recognize a good argument and a bad one.

The mere existence of the Clergy Letter Project, an international organization I founded that is comprised of thousands of clergy members and scientists, demonstrates that religious leaders and scientists are not inherently at odds. After all, more than 12,400 Christian clergy members from all across the United States have signed the Christian Clergy Letter, a powerful, two-paragraph statement promoting a shared understanding and acceptance of evolution and Christianity.

What could be clearer than these sentences from that Letter? "Religious truth is of a different order from scientific truth. Its purpose is not to convey scientific information but to transform hearts[...]. We urge school board members to preserve the integrity of the science curriculum by affirming the teaching of the theory of evolution as a core component of human knowledge. We ask that science remain science and that religion remain religion, two very different, but complementary, forms of truth."

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.